If you're wondering why the cluster is currently unavailable, please see
Paul's message below.
-------- Forwarded Message --------
Subject: [Staff] Compute blade maintenance
Date: Tue, 30 Aug 2016 14:12:09 +0100
From: Paul Elliott <Paul.Elliott(a)ynic.york.ac.uk>
To: undisclosed
Hi all,
I'll shortly be disabling the queues for the cluster so that I can work
with HP to resolve the issues with our compute blades after a further
blade failure overnight. If anybody has any urgent jobs for the cluster
then please let me know and I'll try and work around your jobs.
Thanks, Paul.
--
Paul Elliott, UNIX Systems Administrator
York Neuroimaging Centre (YNiC), University of York
_______________________________________________
Staff mailing list
Staff(a)ynic.york.ac.uk
https://www.ynic.york.ac.uk/mailman/listinfo/staff
Hello All,
You may have already been alerted to this, but I wanted to let you know
that the overhead lighting at YNiC is being replaced today. It is not too
disruptive - I am finding it straightforward to work in open plan.
However, there may be occasions when you will be asked to move so the two
fitters can gain access to a specific ceiling panel.
Best wishes
Tony
--
Antony Morland, PhD
Head of the Centre for Neuroscience, Hull-York Medical School.
Deputy Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Dear colleagues
I am having a clear out before I migrate to another place.
The table in my room has piles of books that are now probably not going
to be read by me again. Feel free to help yourselves.
The ones on my shelf I might read again, or need, so please leave these
for now.
Gary
--
---------------
Gary Green
York Neuroimaging Centre &
Centre for Hyperpolarisation in Magnetic Resonance
The Biocentre
York Science Park
Innovation Way
Heslington
York
YO10 5NY
tel +44 (0) 1904 435349
fax +44 (0) 1904 435356
mobile +44 (0) 788 191 3004
http://www.ynic.york.ac.ukhttp://www.york.ac.uk/chym/https://www.ynic.york.ac.uk/about-us/people/ggrg
Hello All,
David Pitcher will be giving a presentation on two proposed projects; one
TMS and one fMRI.
Best wishes
Tony
--
Antony Morland, PhD
Head of the Centre for Neuroscience, Hull-York Medical School.
Deputy Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Dear all,
Following the cluster failures on Friday we have attempted to replicate
the issue over the weekend by loading up all the compute nodes within
the cluster to the highest level possible. So far we have not seen any
further failures. As such we will shortly return the cluster to service
but as the root cause of the original failures are still unknown we may
see further sudden and unexpected losses of service. If you submit jobs
to the cluster please keep careful track of which jobs you have
submitted and ensure that you validate your jobs have run successfully
before using any of the output.
HP Enterprise (who manufacture and support our hardware) are currently
investigating the cause of the failures and we hope to have a full
resolution as quickly as possible.
Best wishes,
Paul.
--
Paul Elliott, UNIX Systems Administrator
York Neuroimaging Centre (YNiC), University of York
Hello All,
We are having intermittent faults on some of the blades that make up our
cluster. Given that jobs submitted can fail and we also want to ensure no
damage is done to the cluster, we are taking it off line for the time
being. I am very sorry for inconveniences that may arise.
Best wishes
Tony
--
Antony Morland, PhD
Head of the Centre for Neuroscience, Hull-York Medical School.
Deputy Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Dear All,
As you may already know a new Siemens scanner has been installed. Also, we
have hired a new radiographer, Jane. These are both very good pieces of
news for the centre. However, over the summer we will need to run
acceptance testing procedures on the new scanner and also ensure that our
radiographers and other YNiC Staff MRI operators are trained to use the new
scanner. The acceptance testing and training will impact on our provision
of operator covered slots on the GE system. Over this week and last we
have not scheduled operator cover, but have resumed normal operator cover
form 18th July.
We will give as much notice as we can about reductions in operator cover.
If during periods when operator cover is reduced and you need a YNiC to
scan, please get in touch with us and we will do our best to fit you in.
Thanks for your understanding.
Best wishes
Tony
--
Antony Morland, PhD
Head of the Centre for Neuroscience, Hull-York Medical School.
Deputy Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hi all,
It would appear that we may have a 'fault' associated with the new
extension fire doors. They triggered an alarm at the weekend.
Therefore until further notice when locking the department in the
evening please do not set the alarm in the MRI corridor.
Doors should be locked on the computer as per normal and the alarm
should be set in MEG and open plan as usual.
I will update you all when normal procedures can be resumed.
Ross
Hi all,
As the builders are no longer on site, we can now lock the MRI corridor
and its enclosed offices and set the alarm at night.
There are two additional doors which should be 'locked' on the computer
system '1st new extension' and '2nd new extension'.
Many thanks
Ross
http://www.pnas.org/content/pnas/early/2016/06/27/1602413113.abstract.html?…
Functional MRI (fMRI) is 25 years old, yet surprisingly its most common
statistical methods have not been validated using real data. Here, we
used resting-state fMRI data from 499 healthy controls to conduct 3
million task group analyses. Using this null data with different
experimental designs, we estimate the incidence of significant results.
In theory, we should find 5% false positives (for a significance
threshold of 5%), but instead we found that the most common software
packages for fMRI analysis (SPM, FSL, AFNI) can result in false-positive
rates of up to 70%. These results question the validity of some 40,000
fMRI studies and may have a large impact on the interpretation of
neuroimaging results.
They state
"Our principal finding is that the parametric statistical methods work
well, if conservatively, for voxelwise inference, but not for
clusterwise inference. We note that other authors have found RFT
clusterwise inference to be invalid in certain settings under
stationarity (21, 30) and nonstationarity (13, 33). This present work,
however, is the most comprehensive to explore the typical parameters
used in task fMRI for a variety of software tools. Our results are also
corroborated by similar experiments for structural brain analysis (VBM)
(11–13, 39, 40), showing that cluster-based P values are more sensitive
to the statistical assumptions. For voxelwise inference, our results are
consistent with a previous comparison between parametric and
nonparametric methods for fMRI, showing that a nonparametric permutation
test can result in more lenient statistical thresholds while offering
precise control of false positives (13, 41). "
Would be worth discussing at a ynic seminar later in the summer
Gary
--
---------------
Gary Green
York Neuroimaging Centre &
Centre for Hyperpolarisation in Magnetic Resonance
The Biocentre
York Science Park
Innovation Way
Heslington
York
YO10 5NY
tel +44 (0) 1904 435349
fax +44 (0) 1904 435356
mobile +44 (0) 788 191 3004
http://www.ynic.york.ac.ukhttp://www.york.ac.uk/chym/https://www.ynic.york.ac.uk/about-us/people/ggrg
